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Automatic Sequence data extraction?

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  • Automatic Sequence data extraction?

    Hello All,

    I was wondering if anyone knows a way to automatically extract data for multiple species and genes of interest without manual database searches?

    I need to extract DNA sequence data for 5 genes in 36 species. Is there an algorithm/software that allows the names of those genes and species as input and that those genes are automatically searched for sequence data in the databases, extracted and displayed as one file??

    Thanks a lot.

    Cheers
    T

  • #2
    Ensembl certainly have this information available. You can extract information for up to 3 orthologs using BioMart. If you are happy using the Ensembl API then it should be fairly simple to write a script which pulled out the orthologs for a particular gene across the full range of Ensembl species in one go.

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    • #3
      The BIOMART seems inaccessible and I have no clue what API is!! :-(

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      • #4
        http://en.wikipedia.org/wiki/Applica...ming_interface

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        • #5
          Perhaps the compara API from ensembl is a better choice? http://www.ensembl.org/info/docs/api..._tutorial.html
          Look for homology or family.

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          • #6
            Thanks Everyone. I realized that automatic extraction wouldn't work unless I provide specific accession IDs as input since there are multiple versions of every gene (usually). To validate sequence and extract accession IDs, I had to search and visit each entry anyways, so just did it manually!

            Thanks for your quick responses. I appreciate it.

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